title: pTetR VapC26 Replicate 3, 24 hours

city: Bangalore

first: Munmun

last: Bhasin

state: Karnataka

address: CV Raman Rd

department: Molecular Biophysics Unit

country: India

institute: Indian Institute of Science

data_processing:
Data was subjected to quality control check by FastQC
Reads were mapped to H37Rv genome by TopHat
Abundance calculations (FPKM) by Cufflink
Differential expression analysis by Cuffdiff
Visuaization of results by R
Assembly: ASM19595v2 (H37Rv)
Supplementary files format and content: tab-delimited text files include FPKM values for VapC13 overexpression study.
Supplementary files format and content: tab-delimited text files include FPKM values for VapC36 overexpression study.

organism: Mycobacterium tuberculosis H37Rv

source_name: Bacterial Cell lysate

growth_protocol: All strains were grow in 7h9 medium supplemented with 1X ADS (Albumin Dextrose and Saline)

extract_protocol:
RNA was isolated by bead beating the strains in Trizol,  extracted by phenol-chloroform, precipitated with isopropanol and eluted using Qiagen RNA isolation kit
A modified NEBNext RNA Ultra II directional protocol is used to prepare the libraries for total RNAsequencing

treatment_protocol: Overexpreesion of toxins were induced by adding 50 ng/ml Atc for 24 hours

value: Bacterial Cell lysate

value: VapC26 Overexpression


title: pTetR VapC26 Replicate 2, 24 hours

status: Public on May 17 2024

type: SRA

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: genotype


title: 38_D9_3

city: Guangzhou

first: Cuihua

last: Wang

state: Guangdong

address: 601 Huangpu Ave, Guangzhou

country: China

institute: Guangzhou Lab

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the gencode (hg38_enst_v81) transcriptome using STAR (version 2.7)
The gene expression level was calculated by using  STAR
The RNA-seq data processing was performed as described. To analyze the regular gene expression, the reads were aligned to the reference transcriptome by RSEM and bowtie2 (—bowtie2— bowtie2-sensitivity-level very_sensitive —no-bam-output —estimate -rspd) using the index built by RSEM with the mouse genome, mm10, and Ensembl gene annotation track v74
Assembly: hg38
Supplementary files format and content: genes_cpm_expression

organism: Homo sapiens

growth_protocol: H1 hESCs were subjected to EB-primed planar differentiatiation in defined cell culture conditions and in the absence of exogenous hematopoietic cytokines

extract_protocol:
total RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Briefly, to induce hPSC differentiation, 1×106 single cells were spun at 100 × g for 4 minutes (min) into AggreWellTM400 (STEMCELL Technologies) in mTESR1 medium containing 1 μM Thiazovivin (GIBH CAS, China) and incubated for 24 hours at 37°C and 5% CO2. The newly formed clumps were placed on mCollagen IV (Corning Life Sciences, Bedford, MA)–coated surfaces in mTeSR1 medium supplemented with 4 ng/ml hrBMP4 (Peprotech, Rocky Hill, NJ), 50 ng/ml hrVEGF165 (Peprotech) and 10 μM Thiazovivin. After 48 hours, the medium was replaced with StemLineTM II medium (Sigma-Aldrich) supplemented with GlutaMAX®-I (Gibco®, ThermoFisher Scientific, Waltham, MA), 1 × NEAA (Gibco®), 50 µM 2-Mercaptoethanol (Sigma-Aldrich), 50 ng/ml hVEGF165 (Peprotech) and 6 μM SB-431542 (Tocris Bioscience, Bristol, UK). Forty-eight hours later, SB-431542 was removed from the medium. Onward, half of the medium, 2 mL in each well, was replaced with the fresh medium every second day until cell sorting. On Day 12, CD34+ cells were purified by MACS as described above and subjected to the T cell differentiation

tag: time point

tag: cell line

tag: cell type

value: embryonic stem cells

value: KO

tag: treatment

value: blood differentiation


title: pTetR VapC26 Replicate 1, 24 hours


title: 38_D12_1


title: pTetR VapC13 Replicate 3, 24 hours

value: VapC13 Overexpression


title: snRNA_seq_Sham_2

city: Shanghai

first: Yuan

last: Zhang

state: Shanghai

address: 130 Dong an Road, Shanghai 200032, China

institute: Fudan University

library_source: transcriptomic single cell

data_processing:
10X Genomics CellRanger (version 6.1.2)
Seurat
Assembly: mm10
Supplementary files format and content: snRNA-seq:raw feature matrix in Hierarchical Data Format format

molecule: polyA RNA

organism: Mus musculus

source_name: brain; right cortex

growth_protocol: All the mice were housed in IVCs (Individually VentilatedCages) under SPF (Specific Pathogen Free) conditions, with sterile water and food ad libitum on a 12-h dark/light cycle.

extract_protocol:
In this study, for each library, the two right cortices from two mice in the same group were dissected and pooled together for the further nuclei suspension. preparation. After washed by cold 1x PBS, the brain tissue was transferred into the dounce homogenizer containing 5 ml of lysis buffer. After 20 times of up-and-down manual strokes on ice, the homogenized sample was transferred into a new 15 ml conical tube, followed by the centrifugation (4000 r.p.m., 4℃，5min). After centrifugation, the supernatant was discarded, and the precipitation (nuclei pellet) was retained. Then, the 15 ml tube was added with 1 ml of lysis buffer, and the nuclei pellet was pipetted by using a sterile 1 ml pipette tip until the nuclei were well distributed. After the nuclei suspension was added with 4 ml of lysis buffer and 5 ml of sucrose solution sequentially, the nuclei suspension was mixed well by gently inverting the tube ten times. After the centrifugation again (4000 r.p.m., 4℃，5min), the supernatant was discarded, and the precipitation (nuclei pellet) was retained. After the nuclei pellet was resuspended in 1 ml of FBS buffer, the nuclei pellet was pipetted by 1 ml and 200 μl pipette tip until the nuclei were well distributed. After 500 μl of nuclei suspension was taken for being filtered through a 40 μm cell strainer, the nuclei suspension were added 4 ml of FBS buffer. After the first nuclei count, all the nuclei solution was adjusted to a final concentration of 500-1200/μl.
The single-nuclei RNA-seq libraries were prepared using Chromium Single Cell 3ʹ Reagent Kits v3 from 10x Genomics  Single nuclei RNA-seq was performed on DNBSEQ-T7.

treatment_protocol:
The control group was exposed to sham operation
The experimental group was exposed to bilateral carotid artery stenosis (BCAS) operation

tag: strain

value: brain; right cortex

value: WT

value: Sham operation

tag: time

value: 14 weeks


title: pTetR VapC13 Replicate 2, 24 hours


title: snRNA_seq_Sham_1


title: H4006_CT_24h_1

city: Toulouse

first: Juan Pablo

last: Cerapio

address: Av 2 Hubert Curien

country: France

institute: CRCT

data_processing:
bcl2 files conversion to FASTQ format using bcl2fastq algorithm
align to the GRCh38 reference transcriptome using bowtie2
Preprocessing, normalization, QC, and downstream analysis were performed using Deseq2 in R enviroment
The processed (sample x gene) matrix counts are provided.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw counts for every gene and every sample

source_name: lung adenocarcinoma

growth_protocol: The human EGFR-mutant NSCLC PC9, HCC4006, H3255 and HCC827 cell lines were subcloned and amplified in drug-free RPMI (Roswell Park Memorial Institute) 1640 medium containing 10% fetal bovine serum (FBS) and were maintained at 37°C in a humidified chamber containing 5% CO2. Cell lines were authenticated and tested for mycoplasma contamination within the experimental time frame.

extract_protocol:
RNA extraction was performed using AllPrep DNA/RNA Mini kit (Qiagen, #80204) according to the manufacturer’s protocol. RNA quality was assessed using Fragment Analyzer (Agilent technologies) and the RQN values were provided to confirm the integrity of total RNA. RNA concentration was determined by fluorescent method using Quant-iT™ RNA Assay Kit, Broad Range (ThermoFisher Scientific).
RNA samples were processed with Illumina TruSeq® Stranded mRNA Library Preparation Kit following the manufacturer’s protocol. Library size and quality were confirmed on Fragment analyzer (Agilent Technologies). KAPA quantification kit for Illumina platforms (KAPA Biosystems, Roche) was used to quantify the library by qPCR. Indexed libraries were pooled and sequenced on an Illumina NextSeq 550 (2x75 bp paired-end reads).

treatment_protocol: EGFR-mutant NSCLC PC9, HCC4006, H3255 and HCC827 cell lines were subcloned and amplified in drug-free RPMI (Roswell Park Memorial Institute) 1640 medium containing 10% fetal bovine serum (FBS) and were maintained at 37°C in a humidified chamber containing 5% CO2. PC9, HCC4006 and H3255 subclones were treated with DMSO (control) or with erlotinib at 1 µM for 24h, until drug-tolerance (7-to-21 days) or until development of fully resistant proliferative cells (RPC, only for PC9 and HCC4006 cells). RPC were isolated and amplified from individual early-emerging colonies, which were cultured and passaged for more than three months in the presence of the drug. HCC827 were treated with DMSO (control) or with osimertinib at 1 µM until drug-tolerance (11 days).

value: lung adenocarcinoma

value: epithelial cell

tag: subcloned

value: yes

value: DMSO


title: 38_D9_2


title: H3255_NT3


title: 38_D9_1


title: H3255_NT2


title: pTetR VapC13 Replicate 1, 24 hours


title: hapX_a

city: Utrecht

first: Ronald

last: de vries

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: westerdijkinstitute

data_processing:
Clean reads were then mapped to the genome of Aspergillus niger NRRL3 (http://genome.jgi.doe.gov/Aspni_NRRL3_1) using Bowtie2 and HISAT. The gene expression level was measured as Fragments Per Kilobase of transcript per Million mapped reads or FPKM.
Assembly: Aspergillus niger NRRL3 (http://genome.jgi.doe.gov/Aspni_NRRL3_1)
Supplementary files format and content: table-delimited text file including FPKM values

organism: Aspergillus niger

source_name: Mycelium sample

growth_protocol: The strains were pre-grown in complete medium containing 2% (w/v) fructose for 16h. The mycelium was harvested and washed with minimal medium (MM) , and then was transferred to 50 ml MM (pH 6) with 25 mM maltose. After 2h of incubation, the mycelium was harvested and frozen in liquid nitrogen.

extract_protocol:
RNA was extracted from grinded mycelia and were single-end sequenced using Illumina HiSeqTM 2000 platform .
Purification of mRNA, synthesis of cDNA library and sequencing were conducted at the BGI Tech Solutions Co., Ltd. (Hong Kong, China).

value: Mycelium sample

value: delta-hapX

value: cspA1, pyrG-, kusA::amdS, delta-hapX::hph

value: grown on maltose for 2 hour


title: hapX_b


title: WT-PD1-E1

city: Zhengzhou

first: Jiqi

last: Shan

state: Henan

address: 1 Jianshe East Road, Erqi District, Zhengzhou City, Henan Province

institute: The First Affiliated Hospital of Zhengzhou University, Zhengzhou,

data_processing:
Reads were processed using 10X Genomics CellRanger V6.0
Assembly: mm10
Supplementary files format and content: processed gene-cell counts matrix in txt format

source_name: B16 Tumor

extract_protocol:
Cells were extracted according to 10X Genomics compatible protocol. Details can be found in the manuscript.
10X Genomics 3' Kit V2

value: B16 Tumor

value: T cell

value: anti-PD-1 antibody


title: 38_D6_3

value: embryonic stem cells

value: KO

value: blood differentiation


title: ref_b

value: N593 delta-kusA (reference strain)

value: N593 delta-kusA (cspA1, pyrG-, kusA::amdS)


title: pTetR Control Replicate 3, 24 hours

value: Bacterial Cell lysate

value: pTetR harbouring Mycobacterium tuberculosis (H37Rv)


title: 38_D6_2


title: H3255_NT1

value: lung adenocarcinoma

value: epithelial cell


title: ref_a


title: pTetR Control Replicate 2, 24 hours


title: H3255_Erlo_24h_2

value: yes

value: erlotinib 1 uM, 24h


title: 38_D6_1


title: BxPC3 cell line un treated

city: Elizabeth City

first: Hirendranath

last: Banerjee

state: North Carolina

address: 1704 Weeksville Rd,

department: Department of Natural, Pharmacy and Health sciences

country: USA

institute: Elizabeth City State University

data_processing:
Torrent Suite Software v. 5.12.1
Adapters were trimmed and low quality reads filtered by the Torrent Suite Software v. 5.12.1
StrandNGS software v. 3.4
Raw reads were mapped to Hg19 human reference genome using a proprietary algorithm named computationally-optimized Burrows Wheeler Transformed (COBWeb) by the Strand.
Read count extraction and Normalization was performed by StrandNGS using Deseq algorithm.
Assembly: Hg19
Supplementary files format and content: Tab separated value (TSV) text file containing raw counts for each sample.
Library strategy: Ampliseq Transcriptome

source_name: Pancreas

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 10 ng of total RNA was used for the construction of sequencing libraries.
Ampliseq Transcriptome libraries were constructed using the Ampliseq Transcriptome kit (Thermofisher) and manufacturers recommended protocol.

value: Pancreas

value: WT


title: H3255_Erlo_24h_1


title: WT_D16_3


title: BxPC3 cell line Gold Nanoparticle treated

value: Gold Nanoparticle


title: WT_D16_2


title: patient RO, group3, day90

city: Changsha

first: chunwen

last: duan

address: No. 932 Lushan South Road

institute: Central South University

description: PatientC

data_processing:
The raw reads were filtered using SOAPnuke and then stored in a FASTQ format.
The hierarchical indexing for spliced alignment of transcripts (HISAT) was used to align the clean reads to the reference genome (GCF_000001405.39_GRCh38.p13)
The clean reads were aligned to the reference genes by Bowtie2
The expression levels of samples were calculated using the RNA-Seq by Expectation-Maximization (RSEM)
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: The FPKM txt file includes FPKM (log2 (patient / control)) values.

source_name: retinal organoids

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen)
library construction were performed by BGI Tech Solutions Co., Ltd. (Shenzhen, China)

value: retinal organoids

value: XLRS patient hiPSCs

value: hiPSCs

value: without treatment


title: patient RO, group2, day90

description: PatientB


title: WT_D16_1

value: embryonic stem cells


title: HTB172 Cell lines

source_name: Lungs

value: Lungs

value: Lung cancer


title: HTB 172 CELL LINES VANCOMYCIN TREATED

value: Vancomycin


title: patient RO, group1, day90

description: PatientA


title: WT_D12_3

value: blood differentiation


title: Osimertinib+tipifarnib-treated SG2 HCC4006 cells

description:
10X Genomics
SG2_OSI_TIPI_4006

data_processing:
bcl2 files conversion to FASTQ format using cellranger-mkfastq™ algorithm (10x Genomics)
align to the GRCh38 reference transcriptome using cellranger-count
Preprocessing, normalization of UMI, and QC for discarding cell doublets and dying cells were performed using the R package Seurat 4
The integrated (cell x gene) matrices of all single cells are provided.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell for all samples

growth_protocol: The human NSCLC cell lines HCC4006 (CRL-2871, EGFR∆L747-E749, A750P) was obtained from the American Type Culture Collection (ATCC), and cultured in RPMI (Roswell Park Memorial Institute) 1640 medium containing 10% fetal bovine serum (FBS) and were maintained at 37°C in a humidified chamber containing 5% CO2. Cell lines were authenticated and tested for mycoplasma contamination within the experimental time frame. Cells were transduced with the Incucyte® Cell Cycle Green/Red lentivirus based on the FUCCI system, and selected by puromycin treatment for one week.

extract_protocol:
For the experiment, 6 000 cells of each sample were loaded in Chromium device for emulsion-based production of single cell mRNA libraries with the 10X Genomics platform chemistry 3’V2 according to manufacturer’s instructions. Reverse transcription was performed on the C1000 Touch Thermal Cycler, and cDNA were amplified for 12 cycles. cDNA quality control and dosage were performed on Fragment Analyzer, and then by PCR.
single-cell RNA-seq 3’ chemistry; Chromium Controller Single-Cell Instrument and Chromium Single Cell 3' Library & Gel Bead Kit (V2) were used to prepare individually barcoded single-cell RNA-Seq libraries. Double sided size selection of PCR products was performed with SPRIselect Reagent Kit (Beckman Coulter, France). The sequencing-ready library was cleaned up with SPRIselect beads and the sequencing was performed on a NextSeq 550 instrument (Illumina).

treatment_protocol: FUCCI-transduced HCC4006 subcloned cells were expanded in untreated (DMSO), osimertinib (1 µM) or osimertinib (1 µM)  + tipifarnib (1 µM)-containing medium for 4, 20 and 12 days respectively. Drug-containing medium was changed 24h before sorting. Cells were dissociated by trypsinisation, recovered in FACS buffer (0,04% BSA in PBS) and kept on ice. G1 (red) and S/G2 (green) cells were sorted at 4°C using FACS Melody (BD Biosciences).

value: osimertinib 1 µM + tipifarnib 1 µM


title: H3255_Erlo_21j_1

value: lung adenocarcinoma

value: erlotinib 1 uM, 21 days


title: control RO, group2, day90

description: ControlB

value: healthy hiPSCs


title: Cryopreserved 2

city: Faro

first: Elsa

last: Cabrita

state: Faro

address: Universidade do Algarve, Campus de Gambelas

department: Aquaculture research group (Aquagroup)

country: Portugal

institute: Centre of Marine Sciences (CCMAR)

description: column 9

data_processing:
l2fastq v2.20 (Il-lumina Conversion Software) program was used to translate the sequencing reads fromBCL to the standard FASTQ format.
The raw reads were filtered using the BBTols v38.75 software (Bushnell B.). The sequencing adapters, low quality sequences (< Q20) and short sequences (< 40 nucleotides) were removed.
As last filtering step sequences were scanned for traces of ribosomal RNA comingfrom bacteria, eukaryote or archaea with the SortMeRNA v2.1b
As C. angulata whole genome was not available [27], the clean reads were then aligned to the reference genome of Crassostrea gigas (RefSeq accession: GCF_000297895.1 from the NCBI database).
Due to the presence of many isoforms, the quantification of the expression was taken to the gene level, a step performed by the Salmon v1.1 software
Assembly: GCF_000297895.1

organism: Magallana angulata

source_name: D-larvae

growth_protocol: Pooled D-larvae obtained through artificial fertilization were concentrated (around 120,000 larvae per mL) in filtered sea water and kept on ice (4 °C) for a maximum of 2 h.

extract_protocol:
RNA was isolated using TRI Reagent® (Sigma-Aldrich), according to the manufacturer's recommendations, and total RNA was posteriorly purified using the NucleoSpin® RNA II kit (Macherey-Nagel, Germany).
A total of 9 libraries were prepared starting from 1 µg of total RNA using a TruSeq RNA Library Preparation Kit v2 of Illumina (Illumina, USA).

treatment_protocol: As a control group, fresh larvae were concentrated in filtered sea water. In the first treatment, larvae exposed to CPAs, the concentrated D-larvae were diluted in a CPAs consisting in a final concentration of 10% (v/v) dimethyl sulfoxide (DMSO) and incubated for 3 min of equilibrium time, at 4 ºC. The second treatment  followed the same procedure of the first one, the samples were then loaded to 0.5 mL French straws and were frozen in a programable biofreezer.

value: D-larvae

value: Cryopreserved


title: Cryopreserved 3

description: column 10


title: WT_D12_1

value: WT


title: WT_D12_2


title: Osimertinib-treated SG2 HCC4006 cells

description:
10X Genomics
SG2_OSI_4006

value: epithelial cell

value: yes

value: osimertinib 1 µM


title: control RO, group1, day90

description: ControlA

value: retinal organoids

value: hiPSCs


title: Cryopreserved 1

description: column 8


title: pTetR Control Replicate 1, 24 hours

value: Bacterial Cell lysate

value: pTetR harbouring Mycobacterium tuberculosis (H37Rv)


title: WT_D9_3

value: embryonic stem cells


title: H3255_Erlo_21j_3


title: DMSO-treated SG2 HCC4006 cells

description:
10X Genomics
SG2_CTL_4006

value: DMSO


title: Osimertinib+tipifarnib-treated G1 HCC4006 cells

description:
10X Genomics
G1_OSI_TIPI_4006


title: CPA exposed 3

description: column 7

value: CPA exposed


title: WT_D9_2

value: blood differentiation


title: Osimertinib-treated G1 HCC4006 cells

description:
10X Genomics
G1_OSI_4006

value: lung adenocarcinoma


title: GCaMP6f hiPSCs  cir-600-3

city: Syracuse

first: Yuanhui

last: Song

address: 318 Bowne Hall

institute: Syracuse University

data_processing:
The unaligned reads were trimmed for bases to obtain a Phred quality score > 20, and then aligned using the Spliced Transcripts Alignment to a Reference (STAR) to the human genome (hg38).
Assembly: hg38
Supplementary files format and content: tab delimited text files include raw counts for each sample

source_name: skin

growth_protocol: GCaMP6f hiPSCs was maintained in Essential 8 (E8) medium

extract_protocol:
mRNA was extracted using Trizo, Chlorofor), and isopropano.
RNA library was finished by Azenta USA Inc.

treatment_protocol: Cardiac differentiation was initiated (Day 0) when the micropatterns reached confluency and performed via small molecules of GSK3 inhibitor CHIR99021 (Day 0)  and WNT pathway inhibitor IWP4 (Day 2) in RPMI 1640 medium supplemented with B27-minus insulin (RPMI/B27 minus insulin) On Day 6 onward, organoids were maintained in RPMI 1640 medium supplemented with complete B27 supplement (RPMI/B27 Complete) until Day 20 for contractile and structural analysis

value: skin

value: iPSCs lines

value: human induced pluripotent stem cell

value: Cardiac differentiation


title: WT_D9_1

value: WT


title: H3255_Erlo_21j_2

value: epithelial cell

value: erlotinib 1 uM, 21 days


title: GCaMP6f hiPSCs  cir-600-2


title: control RO, group3, day90

description: ControlC

value: healthy  hiPSCs

value: without treatment


title: CPA exposed 1

description: column 5

value: D-larvae


title: WT_D6_3


title: GCaMP6f hiPSCs  cir-600-1


title: CPA exposed 2

description: column 6


title: Fresh 2

description: column 3

value: Fresh


title: Fresh 3

description: column 4


title: GCaMP6f hiPSCs  rec-3


title: WT_D6_2


title: GCaMP6f hiPSCs  rec-2


title: WT_D6_1


title: GCaMP6f hiPSCs rec-1


title: Fresh 1

description: column 2


title: pS129_PFF-treated_mCTXN_rep3

city: Yokohama

first: Sefan

last: Asamitsu

state: Kanagawa

address: 1-7-22, Suehiro-cho, Tsurumi-ku

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

library_source: other

data_processing:
Fastq files were processed for quality check and adapter trimming with the Trimgalore! (v0.6.6).
Trimmed reads were used for mapping to the mouse genome (mm10) using the STAR (v2.7.9a).
RSEM (v1.3.1) was used for obtaining read counts.
DESeq2 (v1.38.3) was used for identifying  BG4-enriched transcripts.
Assembly: mm10
Supplementary files format and content: bigwig

molecule: other

source_name: cortical tissue

extract_protocol:
Primary mouse cortical neurons (mCTXN) treated with vehicle or α-Syn PFF were crosslinked on ice cold RNase free PBS by irradiation with UV light (254 nm) at 150 mJ/cm2. Cells were harvested, lysed, and precleared on DynabeadsTM Protein G (Invitrogen) for 1 hour at 4 ℃. The precleared lysates were incubated at 4°C for three hours in a protein G magnetic beads immobilized with normal rabbit IgG (for control), anti-pS129, or BG4 with anti-DYKDDDDK tag antibody.
Purified protein-bound RNA fraction was subjected to library preparation using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB). All libraries were sequenced on a NextSeq 500 sequencer (illumina).

value: cortical tissue

value: post-mitotic neurons

value: PFF


title: pS129_PFF-treated_mCTXN_rep2


title: pS129_PFF-treated_mCTXN_rep1


title: term-seq_∆rnr_R1

status: Public on May 16 2024

city: Würzburg

first: Cynthia

last: Sharma

state: Bavaria

address: Josef-Schneider-Straße 2

country: Germany

institute: University of Würzburg

data_processing:
Demultiplexing using bcl2fastq (Illumina; version: 2.20.0.422)
Reads were quality and adapter trimmed with Cutadapt (versions: 1.17 and 2.5) (Martin, 2011) using a cutoff Phred score of 20 in NextSeq mode.
READemption (version: 0.4.5) (Förstner et al., 2014) was used to align all reads longer than 11 nt to the reference genome of C. jejuni NCTC11168 (NCBI accession number: NC_002163.1; Refseq assembly accession GCF_000009085.1) using segemehl (version: 0.2.0) (Hoffmann et al., 2009) with an accuracy cutoff of 95%.
READemption (version: 0.4.5) (Förstner et al., 2014) was applied to generate two kinds of positional coverage files: default total coverage based on full-length alignments and last base coverage mapping of only the 3’-end base of each alignment. In both cases, sequencing depth-normalized plots were used for visualization in the Integrated Genome Browser (Freese et al., 2016).
Assembly: ASM908v1
Supplementary files format and content: normalized read coverages in wiggle format with full-length alignment based read coverage (*full coverage_forward.wig = plus strand; *full coverage_reverse.wig = minus strand)
Supplementary files format and content: normalized read coverages in wiggle format with last base coverage mapping of only the 3’-end base of each alignment (*last base_forward.wig = plus strand; *last base_reverse.wig = minus strand)

organism: Campylobacter jejuni

source_name: bacteria

growth_protocol: Bacteria were grown in Brucella Broth (supplemented with 10 µg/ml vancomycin) at 37°C in a microaerobic atmosphere (10% CO2, 5% O2) until log phase.

extract_protocol:
total RNA was treated with DNase I to digest genomic DNA and ribosomal RNA was depleted
3’Term protocol: First, the 5’ Illumina sequencing adapter was ligated to the 3’-OH of the RNA molecules and cDNA synthesis was performed using M-MLV reverse transcriptase. Then, first-strand cDNA was fragmented and the 3’ Illumina sequencing adapter was ligated to the 3’ ends of the single-stranded cDNA fragments. Finally, the 3’ cDNA fragments were PCR-amplified, purified with the Agencourt AMPure XP kit (Beckman Coulter Genomics), and analyzed by capillary electrophoresis.

value: bacteria

value: deltarnr

value: untreated


title: term-seq_∆rny_R2

value: deltarny


title: term-seq_∆rny_R1


title: term-seq_∆pnp_R1

value: deltapnp


title: term-seq_∆rnc_R1

value: deltarnc


title: term-seq_∆pnp_R2


title: term-seq_WT_R2

value: wildtype


title: DMSO-treated G1 HCC4006 cells

description:
10X Genomics
G1_CTL_4006

value: lung adenocarcinoma

value: yes

value: DMSO


title: term-seq_∆rnr_R2


title: RNA-seq_∆rny_R1

data_processing:
Demultiplexing using bcl2fastq (Illumina; version: 2.20.0.422)
Reads were quality and adapter trimmed with Cutadapt (versions: 1.17 and 2.5) (Martin, 2011) using a cutoff Phred score of 20 in NextSeq mode.
READemption (version: 0.4.5) (Förstner et al., 2014) was used to align all reads longer than 11 nt to the reference genome of C. jejuni NCTC11168 (NCBI accession number: NC_002163.1; Refseq assembly accession GCF_000009085.1) using segemehl (version: 0.2.0) (Hoffmann et al., 2009) with an accuracy cutoff of 95%.
Coverage plots representing the number of mapped reads per nucleotide were also generated by READemption and normalized for sequencing depth.
Assembly: ASM908v1
Supplementary files format and content: normalized read coverages in wiggle format with full-length alignment based read coverage (*_forward.wig = plus strand; *_reverse.wig = minus strand)

source_name: Bacteria

extract_protocol:
total RNA was treated with DNase I to digest genomic DNA and ribosomal RNA was depleted
adapter ligation protocol: After ultrasound fragmentation, an adapter was ligated to RNA 3’ ends and reverse transcription was performed, followed by ligation of 5’ Illumina TruSeq sequencing adapters to the 3’ ends of the antisense cDNAs. The resulting cDNA was PCR-amplified, purified with the Agencourt AMPure XP kit (Beckman Coulter Genomics), and analyzed by capillary electrophoresis.

value: Bacteria


title: RNA-seq_WT_R2


title: RNA-seq_WT_R3


title: RNA-seq_∆rny_R2


title: RNA-seq_∆rny_R3


title: RNA-seq_WT_R1


title: peripheral-blood-dna_healthy-control-268

type: genomic

city: Singapore

first: Ann

last: Lee

address: 30 Hospital Boulevard

department: Division of Cellular and Molecular Research

country: Singapore

institute: National Cancer Centre Singapore

description:
healthy volunteer peripheral blood
OU050

hyb_protocol: Bisulfite-converted DNA was amplified and hybridised onto Illumina MethylationEPIC beadchip using standard Illumina protocol

scan_protocol: Arrays were scanned using the Illumina iScan scanner using standard Illumina protocol

data_processing:
Using R/Bioconductor minfi: Probes located near known SNPs of any frequency, or probes known to be cross-reactive were removed. Then, each sample was normalized independently via intra-sample BMIQ normalization.
BMIQ-normalized beta values, after removing probes near SNPs and cross-reactive probes
Unmethylated and methylated signal intensities

label: Cy5, Cy3

molecule: genomic DNA

source_name: Peripheral blood DNA, healthy control 268

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted from whole blood or buffy coat using the Qiagen QIAamp DNA Blood Kit according to standard instructions

tag: condition

value: unaffected


title: peripheral-blood-dna_healthy-control-265

description:
healthy volunteer peripheral blood
OU200

source_name: Peripheral blood DNA, healthy control 265


title: peripheral-blood-dna_healthy-control-262

description:
healthy volunteer peripheral blood
OU209

source_name: Peripheral blood DNA, healthy control 262


title: term-seq_WT_R1


title: peripheral-blood-dna_healthy-control-260

description:
healthy volunteer peripheral blood
DI9

source_name: Peripheral blood DNA, healthy control 260


title: peripheral-blood-dna_healthy-control-263

description:
healthy volunteer peripheral blood
OU069

source_name: Peripheral blood DNA, healthy control 263


title: peripheral-blood-dna_healthy-control-266

description:
healthy volunteer peripheral blood
OU359

source_name: Peripheral blood DNA, healthy control 266


title: peripheral-blood-dna_healthy-control-257

description:
healthy volunteer peripheral blood
DI7_2

source_name: Peripheral blood DNA, healthy control 257


title: peripheral-blood-dna_healthy-control-259

description:
healthy volunteer peripheral blood
DI58

source_name: Peripheral blood DNA, healthy control 259


title: peripheral-blood-dna_healthy-control-264

description:
healthy volunteer peripheral blood
OU174

source_name: Peripheral blood DNA, healthy control 264


title: peripheral-blood-dna_healthy-control-267

description:
healthy volunteer peripheral blood
OU034

source_name: Peripheral blood DNA, healthy control 267


title: peripheral-blood-dna_healthy-control-258

description:
healthy volunteer peripheral blood
DI49

source_name: Peripheral blood DNA, healthy control 258


title: peripheral-blood-dna_healthy-control-256

description:
healthy volunteer peripheral blood
OU046

source_name: Peripheral blood DNA, healthy control 256


title: peripheral-blood-dna_healthy-control-261

description:
healthy volunteer peripheral blood
OU353

source_name: Peripheral blood DNA, healthy control 261


title: term-seq_∆rnc_R2


title: peripheral-blood-dna_healthy-control-255

description:
healthy volunteer peripheral blood
OU328

source_name: Peripheral blood DNA, healthy control 255


title: peripheral-blood-dna_healthy-control-253

description:
healthy volunteer peripheral blood
DI69

source_name: Peripheral blood DNA, healthy control 253


title: peripheral-blood-dna_healthy-control-248

description:
healthy volunteer peripheral blood
OU042

source_name: Peripheral blood DNA, healthy control 248


title: peripheral-blood-dna_healthy-control-250

description:
healthy volunteer peripheral blood
OU288

source_name: Peripheral blood DNA, healthy control 250


title: peripheral-blood-dna_healthy-control-249

description:
healthy volunteer peripheral blood
OU016

source_name: Peripheral blood DNA, healthy control 249


title: peripheral-blood-dna_healthy-control-252

description:
healthy volunteer peripheral blood
DI3_2

source_name: Peripheral blood DNA, healthy control 252


title: peripheral-blood-dna_healthy-control-246

description:
healthy volunteer peripheral blood
OU102

source_name: Peripheral blood DNA, healthy control 246


title: peripheral-blood-dna_healthy-control-251

description:
healthy volunteer peripheral blood
OU012

source_name: Peripheral blood DNA, healthy control 251


title: peripheral-blood-dna_healthy-control-254

description:
healthy volunteer peripheral blood
OU219

source_name: Peripheral blood DNA, healthy control 254


title: peripheral-blood-dna_healthy-control-243

description:
healthy volunteer peripheral blood
BM050

source_name: Peripheral blood DNA, healthy control 243


title: peripheral-blood-dna_healthy-control-245

description:
healthy volunteer peripheral blood
BM039

source_name: Peripheral blood DNA, healthy control 245


title: peripheral-blood-dna_healthy-control-247

description:
healthy volunteer peripheral blood
OU084

source_name: Peripheral blood DNA, healthy control 247


title: peripheral-blood-dna_healthy-control-244

description:
healthy volunteer peripheral blood
DI12_2

source_name: Peripheral blood DNA, healthy control 244


title: peripheral-blood-dna_healthy-control-240

description:
healthy volunteer peripheral blood
DI79

source_name: Peripheral blood DNA, healthy control 240


title: peripheral-blood-dna_healthy-control-241

description:
healthy volunteer peripheral blood
DI32

source_name: Peripheral blood DNA, healthy control 241


title: peripheral-blood-dna_healthy-control-239

description:
healthy volunteer peripheral blood
DI9_2

source_name: Peripheral blood DNA, healthy control 239


title: peripheral-blood-dna_healthy-control-238

description:
healthy volunteer peripheral blood
DI61

source_name: Peripheral blood DNA, healthy control 238


title: peripheral-blood-dna_healthy-control-234

description:
healthy volunteer peripheral blood
DI42

source_name: Peripheral blood DNA, healthy control 234


title: peripheral-blood-dna_healthy-control-235

description:
healthy volunteer peripheral blood
DI39

source_name: Peripheral blood DNA, healthy control 235


title: peripheral-blood-dna_healthy-control-237

description:
healthy volunteer peripheral blood
DI131

source_name: Peripheral blood DNA, healthy control 237


title: peripheral-blood-dna_healthy-control-233

description:
healthy volunteer peripheral blood
DI40

source_name: Peripheral blood DNA, healthy control 233


title: peripheral-blood-dna_healthy-control-236

description:
healthy volunteer peripheral blood
DI134

source_name: Peripheral blood DNA, healthy control 236


title: peripheral-blood-dna_healthy-control-230

description:
healthy volunteer peripheral blood
DI52

source_name: Peripheral blood DNA, healthy control 230


title: peripheral-blood-dna_healthy-control-229

description:
healthy volunteer peripheral blood
BM099

source_name: Peripheral blood DNA, healthy control 229


title: peripheral-blood-dna_healthy-control-227

description:
healthy volunteer peripheral blood
DI120

source_name: Peripheral blood DNA, healthy control 227


title: peripheral-blood-dna_healthy-control-228

description:
healthy volunteer peripheral blood
OU149

source_name: Peripheral blood DNA, healthy control 228


title: peripheral-blood-dna_healthy-control-226

description:
healthy volunteer peripheral blood
OU191

source_name: Peripheral blood DNA, healthy control 226


title: peripheral-blood-dna_healthy-control-231

description:
healthy volunteer peripheral blood
BM106

source_name: Peripheral blood DNA, healthy control 231


title: peripheral-blood-dna_healthy-control-232

description:
healthy volunteer peripheral blood
DI133

source_name: Peripheral blood DNA, healthy control 232


title: peripheral-blood-dna_healthy-control-219

description:
healthy volunteer peripheral blood
DI96

source_name: Peripheral blood DNA, healthy control 219


title: peripheral-blood-dna_healthy-control-225

description:
healthy volunteer peripheral blood
DI81

source_name: Peripheral blood DNA, healthy control 225


title: peripheral-blood-dna_healthy-control-218

description:
healthy volunteer peripheral blood
DI63

source_name: Peripheral blood DNA, healthy control 218


title: peripheral-blood-dna_healthy-control-222

description:
healthy volunteer peripheral blood
DI106

source_name: Peripheral blood DNA, healthy control 222


title: peripheral-blood-dna_healthy-control-220

description:
healthy volunteer peripheral blood
DI97

source_name: Peripheral blood DNA, healthy control 220


title: peripheral-blood-dna_healthy-control-221

description:
healthy volunteer peripheral blood
DI101

source_name: Peripheral blood DNA, healthy control 221


title: peripheral-blood-dna_healthy-control-223

description:
healthy volunteer peripheral blood
DI124

source_name: Peripheral blood DNA, healthy control 223


title: peripheral-blood-dna_healthy-control-242

description:
healthy volunteer peripheral blood
DI7

source_name: Peripheral blood DNA, healthy control 242


title: peripheral-blood-dna_healthy-control-215

description:
healthy volunteer peripheral blood
DI114

source_name: Peripheral blood DNA, healthy control 215


title: peripheral-blood-dna_healthy-control-224

description:
healthy volunteer peripheral blood
DI53

source_name: Peripheral blood DNA, healthy control 224


title: peripheral-blood-dna_healthy-control-213

description:
healthy volunteer peripheral blood
DI117

source_name: Peripheral blood DNA, healthy control 213


title: peripheral-blood-dna_healthy-control-216

description:
healthy volunteer peripheral blood
DI64

source_name: Peripheral blood DNA, healthy control 216


title: peripheral-blood-dna_healthy-control-211

description:
healthy volunteer peripheral blood
DI48

source_name: Peripheral blood DNA, healthy control 211


title: peripheral-blood-dna_healthy-control-210

description:
healthy volunteer peripheral blood
DI30

source_name: Peripheral blood DNA, healthy control 210


title: peripheral-blood-dna_healthy-control-209

description:
healthy volunteer peripheral blood
OU211

source_name: Peripheral blood DNA, healthy control 209


title: peripheral-blood-dna_healthy-control-212

description:
healthy volunteer peripheral blood
DI109

source_name: Peripheral blood DNA, healthy control 212


title: peripheral-blood-dna_healthy-control-214

description:
healthy volunteer peripheral blood
DI130

source_name: Peripheral blood DNA, healthy control 214


title: peripheral-blood-dna_healthy-control-208

description:
healthy volunteer peripheral blood
DI127

source_name: Peripheral blood DNA, healthy control 208


title: peripheral-blood-dna_healthy-control-206

description:
healthy volunteer peripheral blood
DI26

source_name: Peripheral blood DNA, healthy control 206


title: peripheral-blood-dna_healthy-control-207

description:
healthy volunteer peripheral blood
DI25

source_name: Peripheral blood DNA, healthy control 207


title: peripheral-blood-dna_healthy-control-201

description:
healthy volunteer peripheral blood
DI121

source_name: Peripheral blood DNA, healthy control 201


title: peripheral-blood-dna_healthy-control-205

description:
healthy volunteer peripheral blood
DI21

source_name: Peripheral blood DNA, healthy control 205


title: peripheral-blood-dna_healthy-control-204

description:
healthy volunteer peripheral blood
DI4_2

source_name: Peripheral blood DNA, healthy control 204


title: peripheral-blood-dna_healthy-control-203

description:
healthy volunteer peripheral blood
DI89

source_name: Peripheral blood DNA, healthy control 203


title: peripheral-blood-dna_healthy-control-200

description:
healthy volunteer peripheral blood
OU315

source_name: Peripheral blood DNA, healthy control 200


title: peripheral-blood-dna_healthy-control-199

description:
healthy volunteer peripheral blood
BM077

source_name: Peripheral blood DNA, healthy control 199


title: peripheral-blood-dna_healthy-control-198

description:
healthy volunteer peripheral blood
DI129

source_name: Peripheral blood DNA, healthy control 198


title: peripheral-blood-dna_healthy-control-217

description:
healthy volunteer peripheral blood
BM123

source_name: Peripheral blood DNA, healthy control 217


title: peripheral-blood-dna_healthy-control-196

description:
healthy volunteer peripheral blood
OU018

source_name: Peripheral blood DNA, healthy control 196


title: peripheral-blood-dna_healthy-control-192

description:
healthy volunteer peripheral blood
OU202

source_name: Peripheral blood DNA, healthy control 192


title: peripheral-blood-dna_healthy-control-190

description:
healthy volunteer peripheral blood
OU168

source_name: Peripheral blood DNA, healthy control 190


title: peripheral-blood-dna_healthy-control-193

description:
healthy volunteer peripheral blood
OU154

source_name: Peripheral blood DNA, healthy control 193


title: peripheral-blood-dna_healthy-control-191

description:
healthy volunteer peripheral blood
OU173

source_name: Peripheral blood DNA, healthy control 191


title: peripheral-blood-dna_healthy-control-195

description:
healthy volunteer peripheral blood
OU095

source_name: Peripheral blood DNA, healthy control 195


title: peripheral-blood-dna_healthy-control-188

description:
healthy volunteer peripheral blood
OU167

source_name: Peripheral blood DNA, healthy control 188


title: peripheral-blood-dna_healthy-control-189

description:
healthy volunteer peripheral blood
OU262

source_name: Peripheral blood DNA, healthy control 189


title: peripheral-blood-dna_healthy-control-187

description:
healthy volunteer peripheral blood
OU156

source_name: Peripheral blood DNA, healthy control 187


title: peripheral-blood-dna_healthy-control-182

description:
healthy volunteer peripheral blood
OU152

source_name: Peripheral blood DNA, healthy control 182


title: peripheral-blood-dna_healthy-control-185

description:
healthy volunteer peripheral blood
OU048

source_name: Peripheral blood DNA, healthy control 185


title: peripheral-blood-dna_healthy-control-183

description:
healthy volunteer peripheral blood
OU124

source_name: Peripheral blood DNA, healthy control 183


title: peripheral-blood-dna_healthy-control-180

description:
healthy volunteer peripheral blood
OU194

source_name: Peripheral blood DNA, healthy control 180


title: peripheral-blood-dna_healthy-control-186

description:
healthy volunteer peripheral blood
OU130

source_name: Peripheral blood DNA, healthy control 186


title: peripheral-blood-dna_healthy-control-181

description:
healthy volunteer peripheral blood
OU370

source_name: Peripheral blood DNA, healthy control 181


title: peripheral-blood-dna_healthy-control-174

description:
healthy volunteer peripheral blood
DI118

source_name: Peripheral blood DNA, healthy control 174


title: peripheral-blood-dna_healthy-control-175

description:
healthy volunteer peripheral blood
DI20

source_name: Peripheral blood DNA, healthy control 175


title: peripheral-blood-dna_healthy-control-202

description:
healthy volunteer peripheral blood
DI91

source_name: Peripheral blood DNA, healthy control 202


title: peripheral-blood-dna_healthy-control-172

description:
healthy volunteer peripheral blood
DI135

source_name: Peripheral blood DNA, healthy control 172


title: peripheral-blood-dna_healthy-control-178

description:
healthy volunteer peripheral blood
DI5

source_name: Peripheral blood DNA, healthy control 178


title: peripheral-blood-dna_healthy-control-171

description:
healthy volunteer peripheral blood
BM143

source_name: Peripheral blood DNA, healthy control 171


title: peripheral-blood-dna_healthy-control-197

description:
healthy volunteer peripheral blood
BM183

source_name: Peripheral blood DNA, healthy control 197


title: peripheral-blood-dna_healthy-control-194

description:
healthy volunteer peripheral blood
OU015

source_name: Peripheral blood DNA, healthy control 194


title: peripheral-blood-dna_healthy-control-170

description:
healthy volunteer peripheral blood
BM229

source_name: Peripheral blood DNA, healthy control 170


title: peripheral-blood-dna_healthy-control-167

description:
healthy volunteer peripheral blood
BM190

source_name: Peripheral blood DNA, healthy control 167


title: peripheral-blood-dna_healthy-control-168

description:
healthy volunteer peripheral blood
OU226

source_name: Peripheral blood DNA, healthy control 168


title: peripheral-blood-dna_healthy-control-169

description:
healthy volunteer peripheral blood
BM136

source_name: Peripheral blood DNA, healthy control 169


title: peripheral-blood-dna_healthy-control-163

description:
healthy volunteer peripheral blood
DI3

source_name: Peripheral blood DNA, healthy control 163


title: peripheral-blood-dna_healthy-control-165

description:
healthy volunteer peripheral blood
BM159

source_name: Peripheral blood DNA, healthy control 165


title: peripheral-blood-dna_healthy-control-164

description:
healthy volunteer peripheral blood
DI128

source_name: Peripheral blood DNA, healthy control 164


title: peripheral-blood-dna_healthy-control-166

description:
healthy volunteer peripheral blood
BM172

source_name: Peripheral blood DNA, healthy control 166


title: peripheral-blood-dna_healthy-control-184

description:
healthy volunteer peripheral blood
OU140

source_name: Peripheral blood DNA, healthy control 184


title: peripheral-blood-dna_healthy-control-159

description:
healthy volunteer peripheral blood
DI16

source_name: Peripheral blood DNA, healthy control 159


title: peripheral-blood-dna_healthy-control-162

description:
healthy volunteer peripheral blood
DI126

source_name: Peripheral blood DNA, healthy control 162


title: peripheral-blood-dna_healthy-control-158

description:
healthy volunteer peripheral blood
DI2

source_name: Peripheral blood DNA, healthy control 158


title: peripheral-blood-dna_healthy-control-155

description:
healthy volunteer peripheral blood
DI80

source_name: Peripheral blood DNA, healthy control 155


title: peripheral-blood-dna_healthy-control-161

description:
healthy volunteer peripheral blood
DI50

source_name: Peripheral blood DNA, healthy control 161


title: peripheral-blood-dna_healthy-control-157

description:
healthy volunteer peripheral blood
DI8_2

source_name: Peripheral blood DNA, healthy control 157


title: peripheral-blood-dna_healthy-control-154

description:
healthy volunteer peripheral blood
DI56

source_name: Peripheral blood DNA, healthy control 154


title: peripheral-blood-dna_healthy-control-179

description:
healthy volunteer peripheral blood
BM089

source_name: Peripheral blood DNA, healthy control 179


title: peripheral-blood-dna_healthy-control-156

description:
healthy volunteer peripheral blood
DI2_2

source_name: Peripheral blood DNA, healthy control 156


title: peripheral-blood-dna_healthy-control-176

description:
healthy volunteer peripheral blood
DI28

source_name: Peripheral blood DNA, healthy control 176


title: peripheral-blood-dna_healthy-control-177

description:
healthy volunteer peripheral blood
DI1

source_name: Peripheral blood DNA, healthy control 177


title: peripheral-blood-dna_healthy-control-173

description:
healthy volunteer peripheral blood
DI111

source_name: Peripheral blood DNA, healthy control 173


title: peripheral-blood-dna_healthy-control-151

description:
healthy volunteer peripheral blood
DI125

source_name: Peripheral blood DNA, healthy control 151


title: peripheral-blood-dna_healthy-control-153

description:
healthy volunteer peripheral blood
DI116

source_name: Peripheral blood DNA, healthy control 153


title: peripheral-blood-dna_healthy-control-149

description:
healthy volunteer peripheral blood
DI71

source_name: Peripheral blood DNA, healthy control 149


title: peripheral-blood-dna_healthy-control-150

description:
healthy volunteer peripheral blood
DI77

source_name: Peripheral blood DNA, healthy control 150


title: peripheral-blood-dna_healthy-control-146

description:
healthy volunteer peripheral blood
DI47

source_name: Peripheral blood DNA, healthy control 146


title: peripheral-blood-dna_healthy-control-148

description:
healthy volunteer peripheral blood
DI119

source_name: Peripheral blood DNA, healthy control 148


title: peripheral-blood-dna_healthy-control-147

description:
healthy volunteer peripheral blood
DI112

source_name: Peripheral blood DNA, healthy control 147


title: peripheral-blood-dna_healthy-control-144

description:
healthy volunteer peripheral blood
DI66

source_name: Peripheral blood DNA, healthy control 144


title: peripheral-blood-dna_healthy-control-142

description:
healthy volunteer peripheral blood
DI107

source_name: Peripheral blood DNA, healthy control 142


title: peripheral-blood-dna_healthy-control-152

description:
healthy volunteer peripheral blood
DI113

source_name: Peripheral blood DNA, healthy control 152


title: peripheral-blood-dna_healthy-control-140

description:
healthy volunteer peripheral blood
OU005

source_name: Peripheral blood DNA, healthy control 140


title: peripheral-blood-dna_healthy-control-141

description:
healthy volunteer peripheral blood
BM109

source_name: Peripheral blood DNA, healthy control 141


title: peripheral-blood-dna_healthy-control-145

description:
healthy volunteer peripheral blood
DI22

source_name: Peripheral blood DNA, healthy control 145


title: peripheral-blood-dna_healthy-control-160

description:
healthy volunteer peripheral blood
DI110

source_name: Peripheral blood DNA, healthy control 160


title: peripheral-blood-dna_healthy-control-137

description:
healthy volunteer peripheral blood
OU160

source_name: Peripheral blood DNA, healthy control 137


title: peripheral-blood-dna_healthy-control-138

description:
healthy volunteer peripheral blood
OU014

source_name: Peripheral blood DNA, healthy control 138


title: peripheral-blood-dna_healthy-control-136

description:
healthy volunteer peripheral blood
OU011

source_name: Peripheral blood DNA, healthy control 136


title: peripheral-blood-dna_healthy-control-133

description:
healthy volunteer peripheral blood
BM088

source_name: Peripheral blood DNA, healthy control 133


title: peripheral-blood-dna_healthy-control-130

description:
healthy volunteer peripheral blood
OU334

source_name: Peripheral blood DNA, healthy control 130


title: peripheral-blood-dna_healthy-control-143

description:
healthy volunteer peripheral blood
DI73

source_name: Peripheral blood DNA, healthy control 143


title: peripheral-blood-dna_healthy-control-134

description:
healthy volunteer peripheral blood
OU193

source_name: Peripheral blood DNA, healthy control 134


title: peripheral-blood-dna_healthy-control-129

description:
healthy volunteer peripheral blood
BM008

source_name: Peripheral blood DNA, healthy control 129


title: peripheral-blood-dna_healthy-control-128

description:
healthy volunteer peripheral blood
BM139

source_name: Peripheral blood DNA, healthy control 128


title: peripheral-blood-dna_healthy-control-127

description:
healthy volunteer peripheral blood
BM056

source_name: Peripheral blood DNA, healthy control 127


title: peripheral-blood-dna_healthy-control-126

description:
healthy volunteer peripheral blood
BM149

source_name: Peripheral blood DNA, healthy control 126


title: peripheral-blood-dna_healthy-control-125

description:
healthy volunteer peripheral blood
DI13_2

source_name: Peripheral blood DNA, healthy control 125


title: peripheral-blood-dna_healthy-control-135

description:
healthy volunteer peripheral blood
OU271

source_name: Peripheral blood DNA, healthy control 135


title: peripheral-blood-dna_healthy-control-132

description:
healthy volunteer peripheral blood
BM138

source_name: Peripheral blood DNA, healthy control 132


title: peripheral-blood-dna_healthy-control-124

description:
healthy volunteer peripheral blood
DI90

source_name: Peripheral blood DNA, healthy control 124


title: peripheral-blood-dna_healthy-control-123

description:
healthy volunteer peripheral blood
DI62

source_name: Peripheral blood DNA, healthy control 123


title: peripheral-blood-dna_healthy-control-120

description:
healthy volunteer peripheral blood
DI83

source_name: Peripheral blood DNA, healthy control 120


title: peripheral-blood-dna_healthy-control-121

description:
healthy volunteer peripheral blood
OU179

source_name: Peripheral blood DNA, healthy control 121


title: peripheral-blood-dna_healthy-control-118

description:
healthy volunteer peripheral blood
DI15

source_name: Peripheral blood DNA, healthy control 118


title: peripheral-blood-dna_healthy-control-119

description:
healthy volunteer peripheral blood
DI95

source_name: Peripheral blood DNA, healthy control 119


title: peripheral-blood-dna_healthy-control-117

description:
healthy volunteer peripheral blood
OU148

source_name: Peripheral blood DNA, healthy control 117


title: peripheral-blood-dna_healthy-control-116

description:
healthy volunteer peripheral blood
OU183

source_name: Peripheral blood DNA, healthy control 116


title: peripheral-blood-dna_healthy-control-139

description:
healthy volunteer peripheral blood
OU258

source_name: Peripheral blood DNA, healthy control 139


title: peripheral-blood-dna_healthy-control-113

description:
healthy volunteer peripheral blood
BM059

source_name: Peripheral blood DNA, healthy control 113


title: peripheral-blood-dna_healthy-control-112

description:
healthy volunteer peripheral blood
OU355

source_name: Peripheral blood DNA, healthy control 112


title: peripheral-blood-dna_healthy-control-111

description:
healthy volunteer peripheral blood
BM003

source_name: Peripheral blood DNA, healthy control 111


title: peripheral-blood-dna_healthy-control-131

description:
healthy volunteer peripheral blood
OU161

source_name: Peripheral blood DNA, healthy control 131


title: peripheral-blood-dna_healthy-control-109

description:
healthy volunteer peripheral blood
DI78

source_name: Peripheral blood DNA, healthy control 109


title: peripheral-blood-dna_healthy-control-110

description:
healthy volunteer peripheral blood
DI103

source_name: Peripheral blood DNA, healthy control 110


title: peripheral-blood-dna_healthy-control-108

description:
healthy volunteer peripheral blood
DI100

source_name: Peripheral blood DNA, healthy control 108


title: peripheral-blood-dna_healthy-control-107

description:
healthy volunteer peripheral blood
DI99

source_name: Peripheral blood DNA, healthy control 107


title: peripheral-blood-dna_healthy-control-105

description:
healthy volunteer peripheral blood
DI65

source_name: Peripheral blood DNA, healthy control 105


title: peripheral-blood-dna_healthy-control-106

description:
healthy volunteer peripheral blood
DI55

source_name: Peripheral blood DNA, healthy control 106


title: peripheral-blood-dna_healthy-control-103

description:
healthy volunteer peripheral blood
DI87

source_name: Peripheral blood DNA, healthy control 103


title: peripheral-blood-dna_healthy-control-101

description:
healthy volunteer peripheral blood
DI45

source_name: Peripheral blood DNA, healthy control 101


title: peripheral-blood-dna_healthy-control-102

description:
healthy volunteer peripheral blood
DI82

source_name: Peripheral blood DNA, healthy control 102


title: peripheral-blood-dna_healthy-control-104

description:
healthy volunteer peripheral blood
DI59

source_name: Peripheral blood DNA, healthy control 104


title: peripheral-blood-dna_healthy-control-100

description:
healthy volunteer peripheral blood
DI6_2

source_name: Peripheral blood DNA, healthy control 100


title: peripheral-blood-dna_healthy-control-99

description:
healthy volunteer peripheral blood
DI94

source_name: Peripheral blood DNA, healthy control 99


title: peripheral-blood-dna_healthy-control-97

description:
healthy volunteer peripheral blood
BM141

source_name: Peripheral blood DNA, healthy control 97


title: peripheral-blood-dna_healthy-control-122

description:
healthy volunteer peripheral blood
DI92

source_name: Peripheral blood DNA, healthy control 122


title: peripheral-blood-dna_healthy-control-96

description:
healthy volunteer peripheral blood
BM047

source_name: Peripheral blood DNA, healthy control 96


title: peripheral-blood-dna_healthy-control-115

description:
healthy volunteer peripheral blood
DI115

source_name: Peripheral blood DNA, healthy control 115


title: peripheral-blood-dna_healthy-control-91

description:
healthy volunteer peripheral blood
OU054

source_name: Peripheral blood DNA, healthy control 91


title: peripheral-blood-dna_healthy-control-92

description:
healthy volunteer peripheral blood
OU064

source_name: Peripheral blood DNA, healthy control 92


title: peripheral-blood-dna_healthy-control-94

description:
healthy volunteer peripheral blood
OU332

source_name: Peripheral blood DNA, healthy control 94


title: peripheral-blood-dna_healthy-control-114

description:
healthy volunteer peripheral blood
OU090

source_name: Peripheral blood DNA, healthy control 114


title: peripheral-blood-dna_healthy-control-90

description:
healthy volunteer peripheral blood
BM030

source_name: Peripheral blood DNA, healthy control 90


title: peripheral-blood-dna_healthy-control-87

description:
healthy volunteer peripheral blood
DI11

source_name: Peripheral blood DNA, healthy control 87


title: peripheral-blood-dna_healthy-control-89

description:
healthy volunteer peripheral blood
DI19

source_name: Peripheral blood DNA, healthy control 89


title: peripheral-blood-dna_healthy-control-88

description:
healthy volunteer peripheral blood
DI72

source_name: Peripheral blood DNA, healthy control 88


title: peripheral-blood-dna_healthy-control-86

description:
healthy volunteer peripheral blood
DI67

source_name: Peripheral blood DNA, healthy control 86


title: peripheral-blood-dna_healthy-control-85

description:
healthy volunteer peripheral blood
OU062

source_name: Peripheral blood DNA, healthy control 85


title: peripheral-blood-dna_healthy-control-84

description:
healthy volunteer peripheral blood
DI24

source_name: Peripheral blood DNA, healthy control 84


title: peripheral-blood-dna_healthy-control-83

description:
healthy volunteer peripheral blood
DI86

source_name: Peripheral blood DNA, healthy control 83


title: peripheral-blood-dna_healthy-control-82

description:
healthy volunteer peripheral blood
DI74

source_name: Peripheral blood DNA, healthy control 82


title: peripheral-blood-dna_healthy-control-80

description:
healthy volunteer peripheral blood
DI34

source_name: Peripheral blood DNA, healthy control 80


title: peripheral-blood-dna_healthy-control-81

description:
healthy volunteer peripheral blood
DI14

source_name: Peripheral blood DNA, healthy control 81


title: peripheral-blood-dna_healthy-control-77

description:
healthy volunteer peripheral blood
DI11_2

source_name: Peripheral blood DNA, healthy control 77


title: peripheral-blood-dna_healthy-control-98

description:
healthy volunteer peripheral blood
DI84

source_name: Peripheral blood DNA, healthy control 98


title: peripheral-blood-dna_healthy-control-76

description:
healthy volunteer peripheral blood
OU022

source_name: Peripheral blood DNA, healthy control 76


title: peripheral-blood-dna_healthy-control-74

description:
healthy volunteer peripheral blood
DI5_2

source_name: Peripheral blood DNA, healthy control 74


title: peripheral-blood-dna_healthy-control-75

description:
healthy volunteer peripheral blood
DI60

source_name: Peripheral blood DNA, healthy control 75


title: peripheral-blood-dna_healthy-control-95

description:
healthy volunteer peripheral blood
OU109

source_name: Peripheral blood DNA, healthy control 95


title: peripheral-blood-dna_healthy-control-72

description:
healthy volunteer peripheral blood
OU037

source_name: Peripheral blood DNA, healthy control 72


title: peripheral-blood-dna_healthy-control-71

description:
healthy volunteer peripheral blood
OU026

source_name: Peripheral blood DNA, healthy control 71


title: peripheral-blood-dna_healthy-control-73

description:
healthy volunteer peripheral blood
DI88

source_name: Peripheral blood DNA, healthy control 73


title: peripheral-blood-dna_healthy-control-70

description:
healthy volunteer peripheral blood
OU008

source_name: Peripheral blood DNA, healthy control 70


title: peripheral-blood-dna_healthy-control-93

description:
healthy volunteer peripheral blood
DI17

source_name: Peripheral blood DNA, healthy control 93


title: peripheral-blood-dna_healthy-control-69

description:
healthy volunteer peripheral blood
DI6

source_name: Peripheral blood DNA, healthy control 69


title: peripheral-blood-dna_healthy-control-68

description:
healthy volunteer peripheral blood
OU039

source_name: Peripheral blood DNA, healthy control 68


title: peripheral-blood-dna_healthy-control-65

description:
healthy volunteer peripheral blood
DI44

source_name: Peripheral blood DNA, healthy control 65


title: peripheral-blood-dna_healthy-control-67

description:
healthy volunteer peripheral blood
OU047

source_name: Peripheral blood DNA, healthy control 67


title: peripheral-blood-dna_healthy-control-64

description:
healthy volunteer peripheral blood
OU040

source_name: Peripheral blood DNA, healthy control 64


title: peripheral-blood-dna_healthy-control-66

description:
healthy volunteer peripheral blood
OU099

source_name: Peripheral blood DNA, healthy control 66


title: peripheral-blood-dna_healthy-control-63

description:
healthy volunteer peripheral blood
OU031

source_name: Peripheral blood DNA, healthy control 63


title: peripheral-blood-dna_healthy-control-61

description:
healthy volunteer peripheral blood
OU017

source_name: Peripheral blood DNA, healthy control 61


title: peripheral-blood-dna_healthy-control-60

description:
healthy volunteer peripheral blood
DI108

source_name: Peripheral blood DNA, healthy control 60


title: peripheral-blood-dna_healthy-control-62

description:
healthy volunteer peripheral blood
OU336

source_name: Peripheral blood DNA, healthy control 62


title: peripheral-blood-dna_healthy-control-56

description:
healthy volunteer peripheral blood
OU197

source_name: Peripheral blood DNA, healthy control 56


title: peripheral-blood-dna_healthy-control-55

description:
healthy volunteer peripheral blood
OU135

source_name: Peripheral blood DNA, healthy control 55


title: peripheral-blood-dna_healthy-control-58

description:
healthy volunteer peripheral blood
OU301

source_name: Peripheral blood DNA, healthy control 58


title: peripheral-blood-dna_healthy-control-57

description:
healthy volunteer peripheral blood
OU044

source_name: Peripheral blood DNA, healthy control 57


title: peripheral-blood-dna_healthy-control-54

description:
healthy volunteer peripheral blood
OU045

source_name: Peripheral blood DNA, healthy control 54


title: peripheral-blood-dna_healthy-control-79

description:
healthy volunteer peripheral blood
DI29

source_name: Peripheral blood DNA, healthy control 79


title: peripheral-blood-dna_healthy-control-78

description:
healthy volunteer peripheral blood
DI46

source_name: Peripheral blood DNA, healthy control 78


title: peripheral-blood-dna_healthy-control-52

description:
healthy volunteer peripheral blood
OU112

source_name: Peripheral blood DNA, healthy control 52


title: peripheral-blood-dna_healthy-control-51

description:
healthy volunteer peripheral blood
OU126

source_name: Peripheral blood DNA, healthy control 51


title: peripheral-blood-dna_healthy-control-50

description:
healthy volunteer peripheral blood
BM018

source_name: Peripheral blood DNA, healthy control 50


title: peripheral-blood-dna_healthy-control-49

description:
healthy volunteer peripheral blood
DI76

source_name: Peripheral blood DNA, healthy control 49


title: peripheral-blood-dna_healthy-control-46

description:
healthy volunteer peripheral blood
OU141

source_name: Peripheral blood DNA, healthy control 46


title: peripheral-blood-dna_healthy-control-47

description:
healthy volunteer peripheral blood
OU004

source_name: Peripheral blood DNA, healthy control 47


title: peripheral-blood-dna_healthy-control-44

description:
healthy volunteer peripheral blood
BM125

source_name: Peripheral blood DNA, healthy control 44


title: peripheral-blood-dna_healthy-control-45

description:
healthy volunteer peripheral blood
OU205

source_name: Peripheral blood DNA, healthy control 45


title: peripheral-blood-dna_healthy-control-43

description:
healthy volunteer peripheral blood
BM082

source_name: Peripheral blood DNA, healthy control 43


title: peripheral-blood-dna_healthy-control-39

description:
healthy volunteer peripheral blood
BM164

source_name: Peripheral blood DNA, healthy control 39


title: peripheral-blood-dna_healthy-control-34

description:
healthy volunteer peripheral blood
DI43

source_name: Peripheral blood DNA, healthy control 34


title: peripheral-blood-dna_healthy-control-59

description:
healthy volunteer peripheral blood
DI122

source_name: Peripheral blood DNA, healthy control 59


title: peripheral-blood-dna_healthy-control-42

description:
healthy volunteer peripheral blood
DI68

source_name: Peripheral blood DNA, healthy control 42


title: peripheral-blood-dna_healthy-control-37

description:
healthy volunteer peripheral blood
BM060

source_name: Peripheral blood DNA, healthy control 37


title: peripheral-blood-dna_healthy-control-29

description:
healthy volunteer peripheral blood
OU007

source_name: Peripheral blood DNA, healthy control 29


title: peripheral-blood-dna_healthy-control-25

description:
healthy volunteer peripheral blood
OU033

source_name: Peripheral blood DNA, healthy control 25


title: peripheral-blood-dna_healthy-control-38

description:
healthy volunteer peripheral blood
DI132

source_name: Peripheral blood DNA, healthy control 38


title: peripheral-blood-dna_healthy-control-33

description:
healthy volunteer peripheral blood
DI27

source_name: Peripheral blood DNA, healthy control 33


title: peripheral-blood-dna_healthy-control-40

description:
healthy volunteer peripheral blood
OU150

source_name: Peripheral blood DNA, healthy control 40


title: peripheral-blood-dna_healthy-control-31

description:
healthy volunteer peripheral blood
DI70

source_name: Peripheral blood DNA, healthy control 31


title: peripheral-blood-dna_healthy-control-30

description:
healthy volunteer peripheral blood
DI102

source_name: Peripheral blood DNA, healthy control 30


title: peripheral-blood-dna_healthy-control-26

description:
healthy volunteer peripheral blood
OU118

source_name: Peripheral blood DNA, healthy control 26


title: peripheral-blood-dna_healthy-control-41

description:
healthy volunteer peripheral blood
DI123

source_name: Peripheral blood DNA, healthy control 41


title: peripheral-blood-dna_healthy-control-22

description:
healthy volunteer peripheral blood
OU222

source_name: Peripheral blood DNA, healthy control 22


title: peripheral-blood-dna_healthy-control-36

description:
healthy volunteer peripheral blood
DI4

source_name: Peripheral blood DNA, healthy control 36


title: peripheral-blood-dna_healthy-control-32

description:
healthy volunteer peripheral blood
DI93

source_name: Peripheral blood DNA, healthy control 32


title: peripheral-blood-dna_healthy-control-21

description:
healthy volunteer peripheral blood
OU025

source_name: Peripheral blood DNA, healthy control 21


title: peripheral-blood-dna_healthy-control-20

description:
healthy volunteer peripheral blood
BM037

source_name: Peripheral blood DNA, healthy control 20


title: peripheral-blood-dna_healthy-control-23

description:
healthy volunteer peripheral blood
DI23

source_name: Peripheral blood DNA, healthy control 23


title: peripheral-blood-dna_healthy-control-19

description:
healthy volunteer peripheral blood
BM122

source_name: Peripheral blood DNA, healthy control 19


title: peripheral-blood-dna_healthy-control-28

description:
healthy volunteer peripheral blood
OU059

source_name: Peripheral blood DNA, healthy control 28


title: peripheral-blood-dna_healthy-control-27

description:
healthy volunteer peripheral blood
OU061

source_name: Peripheral blood DNA, healthy control 27


title: peripheral-blood-dna_healthy-control-35

description:
healthy volunteer peripheral blood
DI51

source_name: Peripheral blood DNA, healthy control 35


title: peripheral-blood-dna_healthy-control-18

description:
healthy volunteer peripheral blood
OU180

source_name: Peripheral blood DNA, healthy control 18


title: peripheral-blood-dna_healthy-control-17

description:
healthy volunteer peripheral blood
OU053

source_name: Peripheral blood DNA, healthy control 17


title: peripheral-blood-dna_healthy-control-48

description:
healthy volunteer peripheral blood
OU077

source_name: Peripheral blood DNA, healthy control 48


title: peripheral-blood-dna_healthy-control-24

description:
healthy volunteer peripheral blood
OU001

source_name: Peripheral blood DNA, healthy control 24


title: peripheral-blood-dna_healthy-control-53

description:
healthy volunteer peripheral blood
BM035

source_name: Peripheral blood DNA, healthy control 53


title: peripheral-blood-dna_healthy-control-16

description:
healthy volunteer peripheral blood
DI33

source_name: Peripheral blood DNA, healthy control 16


title: peripheral-blood-dna_healthy-control-14

description:
healthy volunteer peripheral blood
DI37

source_name: Peripheral blood DNA, healthy control 14


title: peripheral-blood-dna_healthy-control-15

description:
healthy volunteer peripheral blood
DI31

source_name: Peripheral blood DNA, healthy control 15


title: peripheral-blood-dna_healthy-control-13

description:
healthy volunteer peripheral blood
DI98

source_name: Peripheral blood DNA, healthy control 13


title: peripheral-blood-dna_healthy-control-12

description:
healthy volunteer peripheral blood
DI41

source_name: Peripheral blood DNA, healthy control 12


title: peripheral-blood-dna_healthy-control-6

description:
healthy volunteer peripheral blood
DI38

source_name: Peripheral blood DNA, healthy control 6


title: peripheral-blood-dna_healthy-control-10

description:
healthy volunteer peripheral blood
DI10

source_name: Peripheral blood DNA, healthy control 10


title: peripheral-blood-dna_healthy-control-8

description:
healthy volunteer peripheral blood
DI18

source_name: Peripheral blood DNA, healthy control 8


title: peripheral-blood-dna_healthy-control-5

description:
healthy volunteer peripheral blood
OU074

source_name: Peripheral blood DNA, healthy control 5


title: peripheral-blood-dna_healthy-control-7

description:
healthy volunteer peripheral blood
DI13

source_name: Peripheral blood DNA, healthy control 7


title: peripheral-blood-dna_healthy-control-11

description:
healthy volunteer peripheral blood
DI12

source_name: Peripheral blood DNA, healthy control 11


title: peripheral-blood-dna_healthy-control-9

description:
healthy volunteer peripheral blood
DI36

source_name: Peripheral blood DNA, healthy control 9


title: peripheral-blood-dna_cancer-patient-253

description:
cancer patient peripheral blood
A1129

source_name: Peripheral blood DNA, cancer patient 253

value: affected


title: peripheral-blood-dna_healthy-control-3

description:
healthy volunteer peripheral blood
OU028

source_name: Peripheral blood DNA, healthy control 3


title: peripheral-blood-dna_healthy-control-4

description:
healthy volunteer peripheral blood
OU038

source_name: Peripheral blood DNA, healthy control 4


title: peripheral-blood-dna_cancer-patient-247

description:
cancer patient peripheral blood
BL1330

source_name: Peripheral blood DNA, cancer patient 247


title: peripheral-blood-dna_healthy-control-2

description:
healthy volunteer peripheral blood
OU002

source_name: Peripheral blood DNA, healthy control 2


title: peripheral-blood-dna_healthy-control-1

description:
healthy volunteer peripheral blood
OU006

source_name: Peripheral blood DNA, healthy control 1


title: peripheral-blood-dna_cancer-patient-252

description:
cancer patient peripheral blood
A0967

source_name: Peripheral blood DNA, cancer patient 252


title: peripheral-blood-dna_cancer-patient-256

description:
cancer patient peripheral blood
BS358

source_name: Peripheral blood DNA, cancer patient 256


title: peripheral-blood-dna_cancer-patient-244

description:
cancer patient peripheral blood
BS461

source_name: Peripheral blood DNA, cancer patient 244


title: peripheral-blood-dna_cancer-patient-242

description:
cancer patient peripheral blood
BL519

source_name: Peripheral blood DNA, cancer patient 242


title: peripheral-blood-dna_cancer-patient-251

description:
cancer patient peripheral blood
BL193

source_name: Peripheral blood DNA, cancer patient 251


title: peripheral-blood-dna_cancer-patient-245

description:
cancer patient peripheral blood
BL2259

source_name: Peripheral blood DNA, cancer patient 245


title: peripheral-blood-dna_cancer-patient-246

description:
cancer patient peripheral blood
BL464

source_name: Peripheral blood DNA, cancer patient 246


title: peripheral-blood-dna_cancer-patient-243

description:
cancer patient peripheral blood
BL181

source_name: Peripheral blood DNA, cancer patient 243


title: peripheral-blood-dna_cancer-patient-250

description:
cancer patient peripheral blood
SG1201

source_name: Peripheral blood DNA, cancer patient 250


title: peripheral-blood-dna_cancer-patient-240

description:
cancer patient peripheral blood
BL2403

source_name: Peripheral blood DNA, cancer patient 240


title: peripheral-blood-dna_cancer-patient-239

description:
cancer patient peripheral blood
BL281

source_name: Peripheral blood DNA, cancer patient 239


title: peripheral-blood-dna_cancer-patient-255

description:
cancer patient peripheral blood
A1166

source_name: Peripheral blood DNA, cancer patient 255


title: peripheral-blood-dna_cancer-patient-238

description:
cancer patient peripheral blood
BL820

source_name: Peripheral blood DNA, cancer patient 238


title: peripheral-blood-dna_cancer-patient-237

description:
cancer patient peripheral blood
BL397

source_name: Peripheral blood DNA, cancer patient 237


title: peripheral-blood-dna_cancer-patient-241

description:
cancer patient peripheral blood
BL984

source_name: Peripheral blood DNA, cancer patient 241


title: peripheral-blood-dna_cancer-patient-235

description:
cancer patient peripheral blood
BS594

source_name: Peripheral blood DNA, cancer patient 235


title: peripheral-blood-dna_cancer-patient-232

description:
cancer patient peripheral blood
BS793

source_name: Peripheral blood DNA, cancer patient 232


title: peripheral-blood-dna_cancer-patient-233

description:
cancer patient peripheral blood
BS339

source_name: Peripheral blood DNA, cancer patient 233


title: peripheral-blood-dna_cancer-patient-230

description:
cancer patient peripheral blood
X144

source_name: Peripheral blood DNA, cancer patient 230


title: peripheral-blood-dna_cancer-patient-249

description:
cancer patient peripheral blood
BS740

source_name: Peripheral blood DNA, cancer patient 249


title: peripheral-blood-dna_cancer-patient-236

description:
cancer patient peripheral blood
BL1682

source_name: Peripheral blood DNA, cancer patient 236


title: peripheral-blood-dna_cancer-patient-248

description:
cancer patient peripheral blood
BS682

source_name: Peripheral blood DNA, cancer patient 248


title: peripheral-blood-dna_cancer-patient-227

description:
cancer patient peripheral blood
A1107

source_name: Peripheral blood DNA, cancer patient 227


title: peripheral-blood-dna_cancer-patient-254

description:
cancer patient peripheral blood
A1143

source_name: Peripheral blood DNA, cancer patient 254


title: peripheral-blood-dna_cancer-patient-231

description:
cancer patient peripheral blood
MR0003

source_name: Peripheral blood DNA, cancer patient 231


title: peripheral-blood-dna_cancer-patient-225

description:
cancer patient peripheral blood
A1144

source_name: Peripheral blood DNA, cancer patient 225


title: peripheral-blood-dna_cancer-patient-228

description:
cancer patient peripheral blood
A1171

source_name: Peripheral blood DNA, cancer patient 228


title: peripheral-blood-dna_cancer-patient-223

description:
cancer patient peripheral blood
A0771

source_name: Peripheral blood DNA, cancer patient 223


title: peripheral-blood-dna_cancer-patient-226

description:
cancer patient peripheral blood
A1138

source_name: Peripheral blood DNA, cancer patient 226


title: peripheral-blood-dna_cancer-patient-229

description:
cancer patient peripheral blood
YP25

source_name: Peripheral blood DNA, cancer patient 229


title: peripheral-blood-dna_cancer-patient-224

description:
cancer patient peripheral blood
A0785

source_name: Peripheral blood DNA, cancer patient 224


title: oligomycin_4h-242215

city: Vienna

first: Anastasia

last: Chugunova

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

data_processing:
Reads were preprocessed using umi2index (Lexogen) to add the UMI sequence to the read identifier, and trimmed using BBDuk v38.06 (ref=polyA.fa.gz,truseq.fa.gz k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20). Reads mapping to abundant sequences (mitochondrial chromosome, phiX174 genome, and silva zebrafish rRNAs from the SILVA rRNA database) were removed using bowtie2 v2.3.4.1 alignment.
Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c, alignments were processed using collapse_UMI_bam (Lexogen) and reads in genes were counted with featureCounts (subread v1.6.2) using strand-specific read counting (-s 1) .
Assembly: GRCz11
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Danio rerio

source_name: Embryo

growth_protocol: E3 medium (5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2, 0.33 mM MgSO4, 10−5% methylene blue).

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen, 175023525). 1.5µg of total RNA was used for the construction of sequencing libraries.
Samples were submitted to VBCF NGS facility for library preparation and NGS sequencing. Samples were prepared with Quantseq kit (Lexogen) protocol.

treatment_protocol: Embryos were collected as soon as they were laid and put into E3 medium (5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2, 0.33 mM MgSO4, 10−5% methylene blue) containing inhibitors. Embryos were kept in this medium for the duration of the experiment. For this experiment we used already established concentrations for inhibitors: oligomycin (Millipore, 495455) 1µM, actinomycin D (Sigma-Aldrich, A1410) 10µg/ml. Untreated embryos were kept alongside as controls.

value: Embryo

value: WT (TLAB)

value: oligomycin

value: 4 hpf


title: peripheral-blood-dna_cancer-patient-221

description:
cancer patient peripheral blood
A0176

source_name: Peripheral blood DNA, cancer patient 221


title: peripheral-blood-dna_cancer-patient-222

description:
cancer patient peripheral blood
A0779

source_name: Peripheral blood DNA, cancer patient 222


title: actinomycinD_4h-242212

value: actinomycin D


title: untreated_4h-242211


title: peripheral-blood-dna_cancer-patient-219

description:
cancer patient peripheral blood
A0839

source_name: Peripheral blood DNA, cancer patient 219


title: peripheral-blood-dna_cancer-patient-220

description:
cancer patient peripheral blood
A0860

source_name: Peripheral blood DNA, cancer patient 220


title: peripheral-blood-dna_cancer-patient-234

description:
cancer patient peripheral blood
BL1344

source_name: Peripheral blood DNA, cancer patient 234


title: oligomycin_3h-242209

value: 3 hpf


title: actinomycinD_3h-242206


title: peripheral-blood-dna_cancer-patient-217

description:
cancer patient peripheral blood
X135

source_name: Peripheral blood DNA, cancer patient 217


title: untreated_3h-242205

value: untreated


title: peripheral-blood-dna_cancer-patient-218

description:
cancer patient peripheral blood
BL1335

source_name: Peripheral blood DNA, cancer patient 218


title: peripheral-blood-dna_cancer-patient-216

description:
cancer patient peripheral blood
X199

source_name: Peripheral blood DNA, cancer patient 216


title: peripheral-blood-dna_cancer-patient-214

description:
cancer patient peripheral blood
YP2

source_name: Peripheral blood DNA, cancer patient 214


title: peripheral-blood-dna_cancer-patient-213

description:
cancer patient peripheral blood
YP60

source_name: Peripheral blood DNA, cancer patient 213


title: actinomycinD_4h-242200


title: oligomycin_3h-242197


title: peripheral-blood-dna_cancer-patient-212

description:
cancer patient peripheral blood
YP8

source_name: Peripheral blood DNA, cancer patient 212


title: peripheral-blood-dna_cancer-patient-215

description:
cancer patient peripheral blood
YP31

source_name: Peripheral blood DNA, cancer patient 215


title: peripheral-blood-dna_cancer-patient-210

description:
cancer patient peripheral blood
BL063

source_name: Peripheral blood DNA, cancer patient 210


title: untreated_4h-242199


title: actinomycinD_3h-242194


title: peripheral-blood-dna_cancer-patient-208

description:
cancer patient peripheral blood
A1109

source_name: Peripheral blood DNA, cancer patient 208


title: untreated_3h-242193


title: actinomycinD_4h-239877


title: oligomycin_4h-239880


title: peripheral-blood-dna_cancer-patient-211

description:
cancer patient peripheral blood
BL459

source_name: Peripheral blood DNA, cancer patient 211


title: untreated_4h-239876


title: peripheral-blood-dna_cancer-patient-207

description:
cancer patient peripheral blood
A0427

source_name: Peripheral blood DNA, cancer patient 207


title: peripheral-blood-dna_cancer-patient-209

description:
cancer patient peripheral blood
BL898

source_name: Peripheral blood DNA, cancer patient 209


title: peripheral-blood-dna_cancer-patient-206

description:
cancer patient peripheral blood
A0832

source_name: Peripheral blood DNA, cancer patient 206


title: oligomycin_3h-239874

source_name: Embryo


title: peripheral-blood-dna_cancer-patient-205

description:
cancer patient peripheral blood
MR0010

source_name: Peripheral blood DNA, cancer patient 205


title: peripheral-blood-dna_cancer-patient-203

description:
cancer patient peripheral blood
YP55

source_name: Peripheral blood DNA, cancer patient 203


title: peripheral-blood-dna_cancer-patient-204

description:
cancer patient peripheral blood
FH86

source_name: Peripheral blood DNA, cancer patient 204


title: peripheral-blood-dna_cancer-patient-202

description:
cancer patient peripheral blood
YP63

source_name: Peripheral blood DNA, cancer patient 202


title: oligomycin_4h-239868


title: untreated_3h-239870


title: actinomycinD_4h-239865


title: oligomycin_4h-242203


title: actinomycinD_3h-239871


title: untreated_4h-239864


title: peripheral-blood-dna_cancer-patient-201

description:
cancer patient peripheral blood
HCR015

source_name: Peripheral blood DNA, cancer patient 201


title: oligomycin_3h-239862


title: peripheral-blood-dna_cancer-patient-200

description:
cancer patient peripheral blood
A1123

source_name: Peripheral blood DNA, cancer patient 200


title: actinomycinD_3h-239859


title: peripheral-blood-dna_cancer-patient-199

description:
cancer patient peripheral blood
A1149

source_name: Peripheral blood DNA, cancer patient 199


title: untreated_3h-239858


title: AJ_Palate_Top4_D33mock_biol_rep4

city: Baltimore

first: Suvarna

last: Nadendla

state: MD

address: 670 W.Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland School of Medicine

data_processing:
Reads were mapped to the Mus musculus GRCm39 genome using HISAT.
Gene expression counts were estimated using HTseq. Normalized count data and Variance Stabilized Transformation (VST) counts were generated using the R DESeq2 package.
Assembly: Mus musculus GRCm39
Supplementary files format and content: Tab-delimited file of raw counts

source_name: hard palate

growth_protocol: Sixteen female A/J mice, five weeks old, procured from the Jackson Laboratory (Bar harbor, ME) were acclimatized for one week within the animal facility at Ohio University. Two days prior to N. musculi inoculation, oral swabs and fecal pellets were collected to screen for pre-existing Neisseria flora. No Neisseria spp. were detected after 48 hours of incubation.

extract_protocol:
Mouse hard palates were harvested 5 or 33 days post inoculation or mock inoculation, then were placed in RNA protect (0.5 mL/palate) and snap-frozen in liquid nitrogen. On the day of extraction, mouse palates were removed from RNA Protect, rinsed with cold PBS, then subjected to bead beating using 2-3 3mm glass beads on a TIssueLyser II (4 minutes each side, 20Hz) in 350μL of buffer RLT supplemented with 1% betamercaptoethanol and 20ng of cRNA as a carrier. Debris were pelleted and discarded, and total RNAs were extracted from the supernatant with the Qiagen Micro RNeasy kit. RNAs were quantitated using a Bioanalyzer, then ribosomal RNAs depleted using the NEBNext® rRNA Depletion Kit with bacterial and human/mouse/rat probes mixed at a ratio of 30%/70%, respectively.
Strand-specific, dual unique indexed libraries were made using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA). Manufacturer protocol was modified by diluting adapter 1:30 and using 3μL of this dilution. Library size selection was performed with AMPure SPRI-select beads (Beckman Coulter Genomics, Danvers, MA). Glycosylase digestion of adapter and 2nd strand was done in the same reaction as the final amplification. Libraries were QC’ed using the DNA High Sensitivity Assay on the LabChip GX Touch (Perkin Elmer, Waltham, MA). Library concentrations were also assessed by qPCR using the KAPA Library Quantification Kit (Complete, Universal) (Kapa Biosystems, Woburn, MA).

treatment_protocol: Mice were evenly divided into two groups of eight mice each, consisting of an inoculated group and a control group. Mice in the inoculated group were manually restrained, and a slow oral inoculation of 50μL bacterial suspension was administered, while the control group were mock inoculated with 50μL of PBS into the oral cavity.

value: hard palate

value: Wild type A/J mouse

value: mock colonized with Neisseria musculi

value: Day 33 mock


title: peripheral-blood-dna_cancer-patient-196

description:
cancer patient peripheral blood
A1116

source_name: Peripheral blood DNA, cancer patient 196


title: peripheral-blood-dna_cancer-patient-198

description:
cancer patient peripheral blood
A1115

source_name: Peripheral blood DNA, cancer patient 198


title: AJ_Palate_Top2_D33colonized_biol_rep4

value: colonized with Neisseria musculi, strain NW746

value: Day 33 colonized


title: AJ_Palate_Top3_D5mock_biol_rep4

value: Day 5 mock


title: peripheral-blood-dna_cancer-patient-197

description:
cancer patient peripheral blood
A1054

source_name: Peripheral blood DNA, cancer patient 197


title: peripheral-blood-dna_cancer-patient-194

description:
cancer patient peripheral blood
A1174

source_name: Peripheral blood DNA, cancer patient 194


title: peripheral-blood-dna_cancer-patient-195

description:
cancer patient peripheral blood
A1179

source_name: Peripheral blood DNA, cancer patient 195


title: AJ_Palate_Top1_D5colonized_biol_rep4

value: Day 5 colonized


title: peripheral-blood-dna_cancer-patient-192

description:
cancer patient peripheral blood
A1193

source_name: Peripheral blood DNA, cancer patient 192


title: AJ_Palate_No3_D5mock_biol_rep3


title: AJ_Palate_No4_D33mock_biol_rep3


title: peripheral-blood-dna_cancer-patient-191

description:
cancer patient peripheral blood
A1146

source_name: Peripheral blood DNA, cancer patient 191


title: peripheral-blood-dna_cancer-patient-193

description:
cancer patient peripheral blood
A1100

source_name: Peripheral blood DNA, cancer patient 193


title: AJ_Palate_No2_D33colonized_biol_rep3


title: peripheral-blood-dna_cancer-patient-189

description:
cancer patient peripheral blood
A1197

source_name: Peripheral blood DNA, cancer patient 189


title: peripheral-blood-dna_cancer-patient-188

description:
cancer patient peripheral blood
A1154

source_name: Peripheral blood DNA, cancer patient 188


title: AJ_Palate_Mid4_D33mock_biol_rep2


title: AJ_Palate_Mid2_D33colonized_biol_rep2


title: AJ_Palate_No1_D5colonized_biol_rep3


title: peripheral-blood-dna_cancer-patient-187

description:
cancer patient peripheral blood
A1191

source_name: Peripheral blood DNA, cancer patient 187


title: AJ_Palate_Mid1_D5colonized_biol_rep2


title: peripheral-blood-dna_cancer-patient-190

description:
cancer patient peripheral blood
A1130

source_name: Peripheral blood DNA, cancer patient 190


title: peripheral-blood-dna_cancer-patient-184

description:
cancer patient peripheral blood
A1108

source_name: Peripheral blood DNA, cancer patient 184


title: AJ_Palate_Bottom2_D33colonized_biol_rep1


title: peripheral-blood-dna_cancer-patient-183

description:
cancer patient peripheral blood
A1137

source_name: Peripheral blood DNA, cancer patient 183


title: AJ_Palate_Bottom3_D5mock_biol_rep1


title: AJ_Palate_Bottom4_D33mock_biol_rep1


title: peripheral-blood-dna_cancer-patient-185

description:
cancer patient peripheral blood
A1165

source_name: Peripheral blood DNA, cancer patient 185


title: AJ_Palate_Bottom1_D5colonized_biol_rep1


title: peripheral-blood-dna_cancer-patient-182

description:
cancer patient peripheral blood
A1091

source_name: Peripheral blood DNA, cancer patient 182


title: peripheral-blood-dna_cancer-patient-181

description:
cancer patient peripheral blood
A1188

source_name: Peripheral blood DNA, cancer patient 181


title: P7 cerebellum, rep2

first: Yi

last: Sui

address: South Chongqing Road

institute: Shanghai Jiao Tong University School of Medicine

description:
P7d_2
InVivo_P60+P7+WT_Cerebellum+GDC_Count+FPKM.txt

data_processing:
Trim galore was used to automatically detect and trim adapters.
Reads were mapped to GRCh38 or GRCm38 reference genome using Hisat2.
Counts were generated using HTSeq (version 0.11.1).
Assembly: hg38 for Homo sapiens samples, mm10 for Mus musculus samples.
Supplementary files format and content: txt files included raw counts and FPKM for each Sample

source_name: P7 cerebellum

extract_protocol:
Cells treated with corresponding small molecular inhibitors and mouse cerebellum tissues were harvested and lysed in Trizol. Samples for RNA-seq assays were then sent to MAJORBIO company (Shanghai, China) for RNA extraction.
Samples for RNA-seq assays were sent to MAJORBIO company (Shanghai, China) for library construction and second-generation sequencing.

value: P7 cerebellum

value: Whole cerebellum


title: P60 cerebellum, rep2

description:
P8w_2
InVivo_P60+P7+WT_Cerebellum+GDC_Count+FPKM.txt

source_name: P60 cerebellum

value: P60 cerebellum


title: P60 cerebellum, rep1

description:
P8w_1
InVivo_P60+P7+WT_Cerebellum+GDC_Count+FPKM.txt


title: peripheral-blood-dna_cancer-patient-179

description:
cancer patient peripheral blood
A1167

source_name: Peripheral blood DNA, cancer patient 179

value: affected


title: P7 cerebellum, rep1

description:
P7d_1
InVivo_P60+P7+WT_Cerebellum+GDC_Count+FPKM.txt


title: peripheral-blood-dna_cancer-patient-180

description:
cancer patient peripheral blood
A1121

source_name: Peripheral blood DNA, cancer patient 180


title: peripheral-blood-dna_cancer-patient-178

description:
cancer patient peripheral blood
A1183

source_name: Peripheral blood DNA, cancer patient 178


title: peripheral-blood-dna_cancer-patient-177

description:
cancer patient peripheral blood
A1132

source_name: Peripheral blood DNA, cancer patient 177


title: SmoWT-MB intracranial xenograft, rep1

description:
cereWT_1
InVivo_P60+P7+WT_Cerebellum+GDC_Count+FPKM.txt

source_name: SmoWT-MB intracranial xenograft

value: SmoWT-MB intracranial xenograft

value: mouse SHH-subtype medulloblastoma cells


title: SmoWT-MB intracranial xenograft, rep2

description:
cereWT_2
InVivo_P60+P7+WT_Cerebellum+GDC_Count+FPKM.txt


title: peripheral-blood-dna_cancer-patient-176

description:
cancer patient peripheral blood
A1104

source_name: Peripheral blood DNA, cancer patient 176


title: peripheral-blood-dna_cancer-patient-186

description:
cancer patient peripheral blood
A1173

source_name: Peripheral blood DNA, cancer patient 186


title: AJ_Palate_Mid3_D5mock_biol_rep2

source_name: hard palate


title: peripheral-blood-dna_cancer-patient-175

description:
cancer patient peripheral blood
A1079

source_name: Peripheral blood DNA, cancer patient 175


title: peripheral-blood-dna_cancer-patient-173

description:
cancer patient peripheral blood
A1145

source_name: Peripheral blood DNA, cancer patient 173


title: SMB56, SR4835, 20h, in vitro, rep2

description:
L1EGG260867--B56
InVitro_SMB56_AZD+SR_Count+FPKM.txt

value: 0.5μM SR4835 treated for 20h


title: SmoWT-MB-GR, rep1

description:
L1EFG210271--WTGR01_DMSO_1
SmoWT-GR_Count+FPKM.txt

source_name: SmoWT-MB-GR

value: SmoWT-MB-GR

value: mouse SHH-subtype medulloblastoma cells resistant to GDC-0449

value: 0.1μM GDC-0449 treated for 4 weeks


title: peripheral-blood-dna_cancer-patient-174

description:
cancer patient peripheral blood
A1099

source_name: Peripheral blood DNA, cancer patient 174


title: SMB56, SR4835, 20h, in vitro, rep1

description:
L1EGG260866--B56
InVitro_SMB56_AZD+SR_Count+FPKM.txt


title: peripheral-blood-dna_cancer-patient-172

description:
cancer patient peripheral blood
A1151

source_name: Peripheral blood DNA, cancer patient 172


title: SMB56, AZD4573, 20h, in vitro, rep2

description:
L1EGG260869--B56_AZD01_2
InVitro_SMB56_AZD+SR_Count+FPKM.txt

value: 0.1μM AZD4573 treated for 20h


title: peripheral-blood-dna_cancer-patient-170

description:
cancer patient peripheral blood
A0951

source_name: Peripheral blood DNA, cancer patient 170


title: peripheral-blood-dna_cancer-patient-169

description:
cancer patient peripheral blood
A0911

source_name: Peripheral blood DNA, cancer patient 169


title: SMB56, DMSO, 20h, in vitro, rep1

description:
L1EGG260864--B56_DMSO_1
InVitro_SMB56_AZD+SR_Count+FPKM.txt

value: 0.1% DMSO treated for 20h


title: peripheral-blood-dna_cancer-patient-168

description:
cancer patient peripheral blood
A0796

source_name: Peripheral blood DNA, cancer patient 168


title: peripheral-blood-dna_cancer-patient-166

description:
cancer patient peripheral blood
A1003

source_name: Peripheral blood DNA, cancer patient 166


title: SMB56, GDC-0449, 24h, ex vivo, rep2

description:
SMB56_GDC1uM_24hr_12
ExVivo_56+WT_GDC_Count+FPKM.txt

source_name: SMB56 cells freshly constructed from subcutaneous allograft

value: 1μM GDC-0449 treated for 24h


title: peripheral-blood-dna_cancer-patient-165

description:
cancer patient peripheral blood
A0940

source_name: Peripheral blood DNA, cancer patient 165


title: SMB56, GDC-0449, 24h, ex vivo, rep1

description:
SMB56_GDC1uM_24hr_11
ExVivo_56+WT_GDC_Count+FPKM.txt

value: SMB56 cells freshly constructed from subcutaneous allograft


title: SmoWT-MB-GR, rep2

description:
L1EFG210272--WTGR01_DMSO_2
SmoWT-GR_Count+FPKM.txt


title: SMB56, DMSO, 24h, ex vivo, rep1

description:
SMB56_DMSO_24hr_7
ExVivo_56+WT_GDC_Count+FPKM.txt

value: 0.1% DMSO treated for 24h


title: SmoWT-MB, THZ531, 16h, ex vivo, rep2

description:
P0WT_T5311_2
ExVivo_SmoWT_AZD+T531_Count+FPKM.txt

source_name: SmoWT-MB cells freshly constructed from subcutaneous allograft

value: 1μM THZ531 treated for 16h


title: SmoWT-MB, THZ531, 16h, ex vivo, rep1

description:
P0WT_T5311_1
ExVivo_SmoWT_AZD+T531_Count+FPKM.txt

value: SmoWT-MB cells freshly constructed from subcutaneous allograft


title: peripheral-blood-dna_cancer-patient-163

description:
cancer patient peripheral blood
A0881

source_name: Peripheral blood DNA, cancer patient 163


title: peripheral-blood-dna_cancer-patient-161

description:
cancer patient peripheral blood
A1065

source_name: Peripheral blood DNA, cancer patient 161


title: SmoWT-MB, AZD4573, 16h, ex vivo, rep2

description:
P0WT_AZD01_2
ExVivo_SmoWT_AZD+T531_Count+FPKM.txt

value: 0.1μM AZD4573 treated for 16h


title: peripheral-blood-dna_cancer-patient-160

description:
cancer patient peripheral blood
A1056

source_name: Peripheral blood DNA, cancer patient 160


title: SmoWT-MB, DMSO, 16h, ex vivo, rep2

description:
P0WT_DMSO_2
ExVivo_SmoWT_AZD+T531_Count+FPKM.txt

value: 0.1% DMSO treated for 16h


title: SmoWT-MB, AZD4573, 16h, ex vivo, rep1

description:
P0WT_AZD01_1
ExVivo_SmoWT_AZD+T531_Count+FPKM.txt


title: peripheral-blood-dna_cancer-patient-159

description:
cancer patient peripheral blood
A0973

source_name: Peripheral blood DNA, cancer patient 159


title: peripheral-blood-dna_cancer-patient-158

description:
cancer patient peripheral blood
A0897

source_name: Peripheral blood DNA, cancer patient 158


title: SmoWT-MB, DMSO, 16h, ex vivo, rep1

description:
P0WT_DMSO_1
ExVivo_SmoWT_AZD+T531_Count+FPKM.txt


title: peripheral-blood-dna_cancer-patient-171

description:
cancer patient peripheral blood
A0993

source_name: Peripheral blood DNA, cancer patient 171


title: SMB56, DMSO, 20h, in vitro, rep2

description:
L1EGG260865--B56_DMSO_2
InVitro_SMB56_AZD+SR_Count+FPKM.txt


title: SMB56, AZD4573, 20h, in vitro, rep1

description:
L1EGG260868--B56_AZD01_1
InVitro_SMB56_AZD+SR_Count+FPKM.txt


title: peripheral-blood-dna_cancer-patient-157

description:
cancer patient peripheral blood
A0902

source_name: Peripheral blood DNA, cancer patient 157


title: SmoWT-MB, GDC-0449, i.g., rep2

description:
subWT_G_2
InVivo_P60+P7+WT_Cerebellum+GDC_Count+FPKM.txt

source_name: SmoWT-MB subcutaneous allograft

value: SmoWT-MB subcutaneous allograft

value: GDC-0449, 100 mg/kg, twice daily, i.g.


title: SmoWT-MB, GDC-0449, i.g., rep1

description:
subWT_G_1
InVivo_P60+P7+WT_Cerebellum+GDC_Count+FPKM.txt


title: SmoWT-MB, DMSO, i.g., rep2

description:
subWT_D_2
InVivo_P60+P7+WT_Cerebellum+GDC_Count+FPKM.txt

value: DMSO, 100 mg/kg, twice daily, i.g.


title: peripheral-blood-dna_cancer-patient-155

description:
cancer patient peripheral blood
A0898

source_name: Peripheral blood DNA, cancer patient 155

value: affected


title: peripheral-blood-dna_cancer-patient-167

description:
cancer patient peripheral blood
A1025

source_name: Peripheral blood DNA, cancer patient 167


title: peripheral-blood-dna_cancer-patient-164

description:
cancer patient peripheral blood
A0930

source_name: Peripheral blood DNA, cancer patient 164


title: SMB56, DMSO, 24h, ex vivo, rep2

description:
SMB56_DMSO_24hr_8
ExVivo_56+WT_GDC_Count+FPKM.txt

value: mouse SHH-subtype medulloblastoma cells